Ecological Niche Modeling Course - Academia Sinica, Taipei, Taiwan, 17-19 May 2016.

1. Pleistocene Connectivity of Forest
Distributional Areas: Global
Expectations for Speciation Patterns
A. Townsend Peterson
Biodiversity Institute
University of Kansas

4. Pleistocene Speciation
• Largely discounted based on molecular clock
results, most looking to pre-Pleistocene
conditions
• Refugium thinking … “retreated to refugium
during glacial periods” … dominates
• Evidence solely from molecular data streams
… little or none from independent sources

5. AMAZON BASIN TEST REGION

7. Haffer’s Refugia?
Potential Distribution
21,000 Years Ago
Forest: All Species
Hadley and Canadian
Haffer’s Refugia

8. Schiffornis turdina Complex

9. Present Models and LGM Projections

10. Test Phylogroup Consistency with Refugia

11. Occurrence points

12. Present modeled distribution

13. MIROC model

14. Test Phylogroup-Refugium Coincidence
• Goals – seeking consistency of phylogroup distribution with LGM
Pleistocene refugia
• Assumption – Populations did not undergo broad shifts … i.e., the
lineage of a point falling in a LGM refugium was there at LGM
• Method
– Identify refugia (e.g., disjunct areas at a threshold 10 of 10 models
predicting in a GARP model)
– Overlay points from which molecular sequence data (i.e., of known
phylogroup) were obtained on refugia
– Ignore points falling outside of refugia (they represent hypothesized
dispersal events!)
– Calculate observed degree of coincidence of refugia and phylogroup (i.e.,
how many times do points belonging to the same phylogroup fall in the
same refugium?)
– Calculate degrees of coincidence of ‘refugia’ and phylogroup for 100
randomized replicates …
– Compare observed coincidence with randomized distribution of
coincidences to establish probability values for observed degree of
coincidence

15. Test Phylogroup Consistency with Refugia I
MIROC

16. Test Phylogroup Consistency with Refugia II
Threshold 10

17. Test Phylogroup Consistency with Refugia III
Threshold applied

18. Test Phylogroup Consistency with Refugia IV
Identify refugia by connectivity

19. Test Phylogroup Consistency with Refugia
Overlay phylogroup-specified points

20. Phylogroups
matchputative
refugia
Phylogroupsand
putativerefugia
disagree

21. Amazon Basin – More Detail
• 20 lineages co-distributed across the Amazon
Basin
• Detailed phylogeographic studies with nuclear
and mitochondrial genes sequenced
• Detailed paleo-distributional projections
based on ecological niche models
• Seeking common patterns across multiple taxa

23. Thamnophilus aethiops PRESENT

24. Thamnophilus aethiops LGM / MIROC

25. Thamnophilus aethiops LGM / CCSM

27. Amazon Conclusions
• General coincidence between expectations based
on Pleistocene climate and distributional and
phylogeographic patterns in bird species
• Haffer may have been right in that climate drove
isolation in the Amazon during the Pleistocene
• However, considerable complexity in how
processes were manifested across the region
• Southeastern part so drastically affected as to
extinguish populations

28. COOL AND WARM PERIODS AFFECT
DIFFERENT REGIONS DIFFERENTLY

29. Study Design
• Forest bird species only
• 9 world regions
• Develop models under present conditions
• Test model predictions rigorously in present
• Project to LGM (20K yr ago) and LIG (135K yr
ago)
• Assess fragmentation of populations in each
time period

31. Tangara
mexicana

32. Brachypteracias
leptosomus

33. Aburria
aburri

34. Ducula
carola

35. Now
LGM
LIG
Fragmentation and Speciation Phase
Andes
E Africa
Philippines
Andes
E Africa
Philippines
N America
Amazon
W Africa
Madagascar

37. Results – Species-based Pleistocene History
• Species in some regions fragmented in warm
periods, others in cool periods
• Adjacent regions can be in contrasting phases
(e.g., Andes versus Amazon)
• Speciation in Pliocene was probably not driven
by climatic factors …
• OR time estimates of speciation events are
inaccurate (dramatically)

39. Cyanoderma ruficeps

40. Fig 2. The top row (Current) is the predicted range for each species under contemporary climate patterns. The middle row (LGM) predicts the distribution for each taxa under two climate scenarios
(CCSM3, MIROC), agreement between models is shown with darker colors and areas predicted by only one climate scenario are lighter. The bottom row depicts the predicted distribution for taxa at
the last inter-glacial (LIG).

42. Pomatorhinus ruficollis

43. Conclusions and Next Steps
• Potential for new insights by taking into account
species’ ecological requirements and how their
spatial footprints evolve through time
• Speciation opportunity is out of phase in different
regions
• Pliocene speciation should not be an automatic
conclusion from molecular clock-based inferences
• Continents differ consistently and significantly in
climate stability through time
• Need to incorporate more and richer temporal
data sets … in particular, Pliocene data (3.5M yr
ago, HadCM3) and other ‘older’ data sets
• Need to understand the effects of repeated cycles
of fragmentation and connection on speciation

44. TOWN@KU.EDU